[gmx-users] confusion about pdb file and coordinate.xvg file

[Justin Lemkul]

On 2/4/13 8:06 AM, biki wrote:
> Hi all,
>
> I am doing simulation of 864 spce water molecules in a cubic box of 3nm length in gromacs-4.55 version.
>
> I have generated the trajectory file using trjconv utility in gromacs. Using the  trr file used to generate the .pdb file, I have generated the co-ordinates of H atoms of water using g_traj utility. I thought I will get the same value of co-ordinates of H atoms  in both the files in a particular time step. But it was not so. I am attaching here a part of both the files containing the co-ordinates of H atoms in the first time step. Please note that I have modified and removed the co-ordinates of oxygen atoms from the pdb file. So, Its not exactly the standard format.
>
> My doubts are:
> 1. Am I wrong in thinking that in both the files, co-ordinates of same atoms in a particular time step should be same?
> 2. If I am wrong, then what is correct ?
> 3. If I am correct then  what may be the possible cause of having different coordinates in both the files?
>

The coordinates aren't different in terms of the numbers they actually 
represent.  Gromacs uses nm as a standard unit; PDB files use Angstrom.  Note 
that your numbers are different by exactly a factor of 10.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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